English football has been warned it has allowed one of its major clubs to be exploited as a "branding vehicle" by an international regime accused of human rights abuses after a trial in Abu Dhabi, a country ruled by Manchester City's owner and his brothers, was widely denounced as repressive, involving torture, and "fundamentally unfair".

Amnesty International and Human Rights Watch have vehemently protested against the mass arrest of 94 people, their alleged torture while in Abu Dhabi jails, a "fundamentally unfair" trial, and long prison sentences with no right of appeal handed down earlier this month to the 69 people convicted. Amnesty said the treatment of the 94 in the United Arab Emirates, where Sheikh Mansour al-Nahyan's family, rulers of the richest emirate, Abu Dhabi, are dominant, "shows the authorities' determination to crush any form of dissent".

The 94 were tried on charges of plotting to overthrow the UAE government, which remains adamant this was proven against the 69 convicted. The regime, whose army and security services are headed by Sheikh Mansour's brother, Sheikh Mohammed, the crown prince of Abu Dhabi, maintains the 69 were operating as a front for the Muslim Brotherhood, and seeking to impose a conservative Islamist state, including by military means. The defendants, who include lawyers, teachers and academics, say this was a crackdown by an increasingly authoritarian state, after they voiced valid criticisms of the regime, calling for more democracy and freedom of speech. Only a minority of the UAE population has any kind of vote, the ruling families have been in charge for centuries, and in 2013 it remains a crime to criticise the rulers, belong to a trade union or form any organisation not licensed by the regime.

Amnesty and HRW have stated that they believe torture is "a systematic practice" in Abu Dhabi and UAE state security jails, and that complaints that these men were tortured, including to extract confessions, have not been investigated. Amnesty said the trial showed "a deeply flawed judicial system" at odds with the "global image the UAE likes to project of itself as an efficient, forward-thinking country, which in many ways it is".

HRW made specific reference to Manchester City, arguing that ownership of the Premier League club is enabling Abu Dhabi to "construct a public relations image of a progressive, dynamic Gulf state, which deflects attention from what is really going on in the country".

Sheikh Mansour bought City in 2008, and has since spent around £1bn of the fortune he wields as a member of Abu Dhabi's ruling family, principally to buy and pay the multimillion-pound wages of footballers to make City successful. Mansour is among the most powerful group in Abu Dhabi with the crown prince Sheikh Mohammed and their other "full" brothers by Sheikha Fatima, one of the six wives married to the former ruler, Sheikh Zayed bin Sultan al-Nahyan. Sheikh Khalifa, Zayed's oldest son, one of Mansour's half-brothers by a different wife, is the UAE president, said to be ailing in health. Mansour is the Abu Dhabi deputy prime minister, responsible for the country's judges, and sits on the board of key investment funds.

Manchester City is run by Khaldoon al-Mubarak, the chairman, a senior Abu Dhabi government and business figure, who works principally for Sheikh Mohammed. Mubarak is the chairman of the Executive Affairs Authority, a strategic government body responsible for advising on Abu Dhabi's international image. He was deputed from his duties for Sheikh Mohammed to run City shortly after Mansour bought the club, to shape a more dignified direction after the initial frenzy of media coverage which was all about money and considered detrimental by the Abu Dhabi establishment.

Mubarak has always emphasised that City is a private business acquisition by Sheikh Mansour, with Mubarak charged to make it profitable, worth more than the £1bn spent, in 10 years. The Premier League club, though, have unquestionably become the most prominent global projection of Abu Dhabi itself, sponsored by four state-owned companies: the airline Etihad, the telecommunications company Etisalat, the investment company Aabar and the Abu Dhabi Tourism Authority. When David Silva, Sergio Agüero and Yaya Touré weave their patterns in the Etihad Stadium, the hoardings around the pitch beam "Visit Abu Dhabi, Travellers Welcome" to the 200 countries where Premier League football is viewed – a great global advert.

In an interview with the Guardian in 2009, Mubarak said of the running of City: "This is telling a lot to the world about how we are. It is showing the world … the true essence of … what Abu Dhabi is about. There is almost a personification of the values we hold as Abu Dhabi, with the values of the club and the values we would like to stick to."

Nicholas McGeehan, UAE researcher for HRW, describes the country in the light of the recent trial as increasingly "a black hole" for many basic human rights: "In this situation, a Premier League club is being used as a branding vehicle to promote and effectively launder the reputation of a country perpetrating serial human rights abuses," he said. "That should be of concern to football supporters as well as human rights organisations."

This condemnation of the UAE for a crackdown on citizens criticising the ruling regime is relatively recent. An alliance of seven emirates made in 1971, the UAE's native Emirati people have generally been considered content with their stable and wealthy way of life. Sheikh Zayed, who died in 2004, was widely revered as a visionary, planning Abu Dhabi's super-fast development after the oil riches transformed the country from the 1960s, while retaining traditional Sunni Muslim values. Zayed distributed wealth to the wider population and, although democracy has always been outlawed, he famously talked of gradually introducing voting rights: "Moving towards a parliamentary, integrated and comprehensive system in a society liberated from fear."

HRW's previous concerns have centred on low pay and grim conditions for the people from India, Pakistan, Bangladesh and elsewhere brought to the UAE to build its prestige buildings, and work in domestic service. In a series of reports, HRW has highlighted exploitative practices, including burdensome recruitment fees charged to workers before they arrive, low pay of around $8 a day in one of the world's richest countries, the prevailing system of being tied to one employer, and the prohibition on forming a union or striking for better terms.

The government has repeatedly acknowledged the criticisms, and says: "Sweeping reforms aimed at improving working conditions and worker rights reflect the UAE's commitment to treat all guest workers with dignity and respect."

HRW argues that is not matched by the reality and points to continuing reports of construction workers being deported after going on strike over low pay and dreadful working conditions on projects in the UAE.

The Emirati population, which numbers around one million, are still considered by commentators to be largely content, particularly given the country's stability in a Middle East in turmoil and civil war elsewhere. But internal critics began to find more of a voice two years ago, against a background of the Arab spring, conservative Muslim campaigns and democracy movements in other countries, allied to widespread use of the internet.

In March 2011, five Emiratis posted a petition addressed to Sheikh Khalifa, the UAE president. The petition expressed profound respect for Khalifa and the Federal Supreme Council, the law-making organ of state run by the seven emirates' ruling families. Quoting Zayed's vision of a parliamentary system for "a society liberated from fear," the petition asked for greater democracy, by: "Electing all the members of the Federal Supreme Council by all citizens in the same manner that is approached in the democratic countries around the world." The UAE authorities argue it was not the petition itself that led to those posting it being arrested but the continued criticism with which they followed it up.

One of the most persistent, Ahmed Mansoor, was kept in jail for eight months before being sentenced to three years in prison for criticising the regime. Immediately after his sentence Mansoor, along with the other petitioners, received a presidential pardon.

"I am a liberal secularist and do not belong to any religious group," Mansoor told the Guardian. An engineer who studied at the University of Colorado and lived in the US for seven years, when Mansoor returned to his native UAE he found its lack of democracy and freedom of speech stifling.

"I, with another person, initiated the petition, then I was subjected to a smear campaign, arrested for comments deemed to be insulting to the president, and put in jail," he said. "I lost my job, I have been beaten up twice, so I am paying a high price. But I feel I must talk.

"It is a very difficult and ugly feeling when you cannot express yourself because you are in fear of being arrested. The state security apparatus can be very ugly, so people are really afraid to say anything."

The authorities argue there is no connection between that case of the "UAE 5", and the arrests and prosecution of the "UAE 94" that followed last year. The people arrested were mostly members of a long-established Muslim social organisation, al-Islah, who say they are not fundamentalist but do openly take issue with elements of the country's rule. They argue that the super-capitalist development has been done without sufficient consultation and is a departure too far from traditional Muslim values, that the ruling family is not accountable for how the country's money is spent, and that freedom is too limited. As they include middle-aged, educated people, they say it is ridiculous to accuse them of believing they could overthrow the regime, given the wealth, might and security apparatus of the UAE.

Last summer, after the number of people arrested had grown to over 50, the official Emirates News Agency stated that the security services' investigation revealed that those arrested had "set up links with external elements, and had worked in an organised and systematic manner, causing harm to the country and spreading false information, in order to incite others against the country and to distort its shining image before the world".

In July two lawyers who had defended Ahmed Mansoor in the "UAE 5" trial, Dr Mohamed al-Mansoori and Dr Mohamed al-Roken, were arrested. In December, the International Bar Association's Human Rights Institute issued a statement saying it was "deeply concerned by the worsening situation for human rights lawyers in the UAE." The British barrister Baroness Kennedy, co-chair of IBAHRI, said: "Disturbing reports of an increasing catalogue of detention, deportation, intimidation and harassment of lawyers by the UAE authorities is creating a climate of fear among the legal profession – seriously undermining the rule of law in the country."

HRW expressed concerns that the families of most of those arrested did not know where they were for months, and warned there is a close relationship between prisoners held incommunicado and mistreatment. Six of the 94 detainees finally appeared before a judge in Abu Dhabi on 6 September 2012 and were reported by HRW and Amnesty to have appeared "dishevelled, disoriented and distressed".

At the first court hearing on 4 March 2013 in Abu Dhabi, Amnesty and HRW reported that several defendants told the judge they had been "seriously ill-treated during months in detention". They described prolonged solitary confinement, hooding, sleep deprivation and being subjected to extremes of temperatures. The report said the judge ordered medical examinations of the defendants, so the allegations could be investigated, but both human rights groups say no such investigation has taken place.

On 26 June, Amnesty and HRW issued their most serious statement on the case, detailing allegations of "systematic" torture, based on hand-written letters smuggled out of the jails. "The mistreatment described in the letters is consistent with other allegations of torture at UAE state security facilities," the statement said, "and indicates that torture is a systematic practice at these facilities".

The accounts tallied with previous allegations of torture that HRW had reported in September, along with the alleged disappearance of one of the 94, Ahmed al‑Suweidi. Amnesty and HRW said "local activists believe a forced confession from Suweidi forms the basis of the prosecution's case in the trial".

At the 4 March hearing, Suweidi had reportedly told the judges: "I know that what I'm going to say may cost my life but I deny the charges and I ask the court to protect my life and the life of my family."

On 10 June 2012, another Emirati, Saud Kulaib, tweeted that Suweidi was "being exposed to severe torture under the supervision of a high official". Kulaib was arrested in December and, according to HRW and Amnesty, held incommunicado for five months, during which time he alleged he was held in solitary confinement, subjected to extremes of temperature and sleep deprivation, suspended by his legs from an iron rod and severely beaten by officers, including having his hand sliced open with a razor blade.

Other allegations of torture included one detainee saying he was "beaten with a plastic tube all over my body"; another wrote he was tied to a chair and threatened with electrocution. The human rights organisations called on the UAE authorities to provide independent medical examinations of the detainees who claimed to have been tortured, exclude from the proceedings any evidence obtained by torture, and carry out a prompt investigation. Both Amnesty and HRW say none of that has happened.

The UAE authorities' response to the torture allegations, which were raised in court, is to argue that the alleged victims should have reported them to the police. "The UAE judicial system ensures that the rule of law prevails and that no person is above the law," the Ministry of Justice said in a statement. "Therefore anyone can resort to the public authorities to report assault, request protection, or claim compensation and ensure that any person committing any offence or felony is punished under law."

On 2 July, at the Federal Supreme Court in Abu Dhabi, 69 of the 94 were found guilty of plotting to overthrow the regime. Several were given severe sentences, including the lawyers Mohamed al-Roken and Mohamed al-Mansoori, both sent to prison for 10 years.

Amnesty and HRW denounced the "mass trial of 94 government critics", arguing that the convictions were: "Based on a fundamentally unfair trial … probably violated the right of free association … was marred by the denial of legal assistance during pretrial incommunicado detention, and allegations of torture."

On 17 July, Katherine Dine, a British government official, wrote to Rori Donaghy, campaign manager at the UK-based Emirates Centre for Human Rights, which is pressing the case of the convicted. Dine wrote that the British government has followed the trial closely, and the foreign secretary, William Hague, had: "Raised the importance of … ensuring the human rights of all Emirati citizens are fully respected. We along with others, have made clear our concerns about allegations of torture and mistreatment, and some aspects of the way the trial was conducted, such as lack of access to international observers, accusations that defendants could not access their lawyers, and the length of the sentencing."

The UAE authorities have maintained there was due process and a fair trial. Anwar Gargash, the UAE minister of state for foreign affairs, has rejected critics of the regime, arguing they do not give enough credit for the UAE's achievements, including the "secure and stable livelihood" the UAE enables its residents to have in a trouble-torn region.

Gargash explained that the UAE regime does not believe in democracy, with political parties, arguing they descend into tribal division and sectarianism. "There is insufficient evidence that a multiparty system works in the Arab world," Gargash said.

He pointed to "gradual" reforms including "limited" elections of the Federal National Council, a consultative body, of which half the members are selected by the regime, half elected by a minority of the Emirati population. "To the critics of the approach, we say that it enjoys the support of the majority of our citizens," Gargash said.

How all this strife and struggle over the rulers by birth of a complex, faraway country ended up washing into the fabric of Manchester City is a story of our times. Whereas Manchester became the world's first industrial city in the 1800s, Abu Dhabi did not have a paved road until 1961, when its deep reserves of oil began to be exploited. In Manchester at the "Peterloo Massacre" of 1819, 11 people were killed and 600 injured by cavalry when attending a speech by Henry Hunt, a campaigner for adults to have the vote. "All men are born free, equal and independent of each other," Hunt had declared before the forces charged.

Another landmark of Mancunian pride is the city's struggle for workers' rights, the first meeting of the Trades Union Congress having been held in Manchester in 1868. The two great Manchester football clubs emerged from this industrial tumult and social progress; United formed with the approval of employers at the Lancashire and Yorkshire Railway in 1878, City two years later by Anna Connell, vicar's daughter at St Mark's church, Gorton, part of an effort to provide some decent recreation in the toughest of neighbourhoods.

Manchester suffered catastrophically in the 1980s from the collapse of its industry, with 150,000 jobs lost, particularly in the east of the city, which has never recovered. In a UK and Europe again in economic depression after the banking collapse, the real wealth from the oil and gas-rich Gulf states is eagerly sought, not only in football. The Abu Dhabi cash and Mubarak's and his other executives' business expertise are transforming not only Manchester City but the stadium that was built with £127m lottery and local council money for the 2002 Commonwealth Games as a means of regenerating east Manchester. Sheikh Mansour's money is now building a £140m training campus on 80 acres of largely derelict land, the most significant private business investment into east Manchester for years.

In this meeting, of a desperate UK economy with Abu Dhabi's fortunes, there is a limit to the UK government's disapproval over allegations of torture and flaws in the UAE legal system. In November, David Cameron flew to Dubai, seeking to persuade the UAE government to buy 60 Typhoon fighters from UK companies in a deal reckoned to be worth £3bn. In London on 16 July, a fortnight after the 69 defendants were convicted in the UAE, the crown prince, Sheikh Mohammed, was in London, meeting Philip Hammond, the British defence secretary, to discuss "co-operation between the two countries pertaining to military and defence affairs." Mubarak accompanied Sheikh Mohammed to that meeting.

The former Football Association chairman Lord Triesman proposed including in the sports authorities' "fit and proper person test" for club owners consideration of HRW's human rights reports by country. The Premier League rejected that proposal but says it does ask the government about owners – and will have been told that the UAE is a trusted ally.

"When a prospective takeover is from overseas we confirm that those involved are legally permitted to invest in this country," a Premier League spokesman said, "and, when appropriate, seek the advice of the Foreign and Commonwealth Office."

The major northern football clubs have flourished on pay TV after so much industry collapsed around them but the Premier League's economics are such that clubs, Arsenal in the Emirates Stadium apart, struggle to compete against Manchester United's dominant wealth without a billionaire's backing. While Arsenal, United and Chelsea are nearing the start of this Premier League season still publicly talking about bids for big-name players, City have quietly spent £87m on four stars for the new manager, Manuel Pellegrini. Fernandinho, £30m from Shakhtar Donetsk, Jesús Navas, £15m from Sevilla, Stevan Jovetic, £22m from Fiorentina and Alvaro Negredo, £20m, also from Sevilla, have been assembled to renew Sheikh Mansour's intentions for City to achieve Premier League and European success.

The reconstruction has been done with a care to appreciate the fans' loyalty through City's long-suffering years and to celebrate the club's heritage and former players in ways no previous Manchester owners ever managed. The owner has still been to only one match in five years, instead watching his team's ascent on television, but the City supporters long ago made clear their feelings about the Abu Dhabi ownership. In 2009, some fans clubbed together to pay for a banner, draped ever since along the stand opposite the directors' box. In huge white letters on a sky blue background, it says: "MANCHESTER THANKS YOU, SHEIKH MANSOUR."